Every generation has multiple games covering the same story with only a few differences. Which game of each gen do you consider as the 'correct' version of the story? For me it's this.
Generation 1, Red: it is nearly the same as Blue version but the only reason I consider Red version the actual one is because the protagonist name is Red and the rival is Blue.
Generation 2, Gold: even though I played more of Silver and Crystal than Gold I still consider Gold to be the actual story. There is just a lot more build up for Ho-Oh than for Lugia and Suicune.
Generation 3, Emerald: Emerald is pretty much the stories of Ruby and Sapphire combined, which I like more than disproving one of the two teams.
Generation 4, Platinum: in this version all three of the creation trio get substantial coverage instead of only one.
Generation 5, Black and Black 2: the only reason for this is that I think N fits better with Reshiram than with Zekrom.
Generation 6, X: Xerneas feels a bit more fleshed out than Yveltal.
Generation 1, Red: it is nearly the same as Blue version but the only reason I consider Red version the actual one is because the protagonist name is Red and the rival is Blue.
Generation 2, Gold: even though I played more of Silver and Crystal than Gold I still consider Gold to be the actual story. There is just a lot more build up for Ho-Oh than for Lugia and Suicune.
Generation 3, Emerald: Emerald is pretty much the stories of Ruby and Sapphire combined, which I like more than disproving one of the two teams.
Generation 4, Platinum: in this version all three of the creation trio get substantial coverage instead of only one.
Generation 5, Black and Black 2: the only reason for this is that I think N fits better with Reshiram than with Zekrom.
Generation 6, X: Xerneas feels a bit more fleshed out than Yveltal.